ClinVar Miner

Submissions for variant NM_000286.3(PEX12):c.538C>T (p.Arg180Ter)

gnomAD frequency: 0.00003  dbSNP: rs61752103
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000666018 SCV000790249 pathogenic Peroxisome biogenesis disorder type 3B; Peroxisome biogenesis disorder 3A (Zellweger) 2017-03-08 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000666018 SCV000894112 pathogenic Peroxisome biogenesis disorder type 3B; Peroxisome biogenesis disorder 3A (Zellweger) 2018-10-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001193474 SCV001362342 pathogenic Peroxisome biogenesis disorder 2019-10-14 criteria provided, single submitter clinical testing Variant summary: PEX12 c.538C>T (p.Arg180X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 3.6e-05 in 251490 control chromosomes (gnomAD). c.538C>T has been reported in the literature in individuals affected with Zellweger Syndrome (Okumoto_1998, Chang_1998, Schabhuttl_2014, Gootjes_2004, Dranchak_2011). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000008216 SCV001581547 pathogenic Peroxisome biogenesis disorder 3A (Zellweger) 2024-01-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg180*) in the PEX12 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX12 are known to be pathogenic (PMID: 9090384, 9632816, 21031596). This variant is present in population databases (rs61752103, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with clinical features of Zellweger syndrome (PMID: 9792857, 24627108). ClinVar contains an entry for this variant (Variation ID: 7774). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000008216 SCV004201427 pathogenic Peroxisome biogenesis disorder 3A (Zellweger) 2024-03-27 criteria provided, single submitter clinical testing
OMIM RCV000008216 SCV000028423 pathogenic Peroxisome biogenesis disorder 3A (Zellweger) 2004-06-08 no assertion criteria provided literature only
OMIM RCV000032926 SCV000056698 pathogenic Peroxisomal biogenesis disorder 3b 2004-06-08 no assertion criteria provided literature only

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